GTDT - Revision history

Bingshan: /* Input */

2015-03-26T12:18:54Z

Input

← Older revision		Revision as of 08:18, 26 March 2015
Line 76:		Line 76:
	* A group file indicating which variants should be analyzed as a unit. It has required 3 columns, plus additional columns for weighting and others. For example:		* A group file indicating which variants should be analyzed as a unit. It has required 3 columns, plus additional columns for weighting and others. For example:

	CHR POS Group		#CHR POS Group
	1 10000 gene1		1 10000 gene1
	1 20000 gene1		1 20000 gene1
Line 85:		Line 85:
	If you have specific weights for each variant you can provide on column 4.		If you have specific weights for each variant you can provide on column 4.

	CHR POS Group WEIGHT		#CHR POS Group WEIGHT
	1 10000 gene1 2.1		1 10000 gene1 2.1
	1 20000 gene1 2.5		1 20000 gene1 2.5

2015-01-09T19:25:40Z

Introduction

← Older revision		Revision as of 15:25, 9 January 2015
Line 3:		Line 3:

	* The 6 models are described as follows		* The 6 models are described as follows
	M1: additive model with equal weights (sum statistics)		AD: additive model with equal weights (sum statistics)
	M2: additive model with unequal weights (weighted sum statistics)		wAD: additive model with unequal weights (weighted sum statistics)
	M3: dominant model (i.e. carriers vs. non-carrier, or indicator model, or collapsing model)		DOM: dominant model (i.e. carriers vs. non-carrier, or indicator model, or collapsing model)
	M4: compound heterozygous model (CH), also 2-hits or multi-hits models, or recessive model.		CH: compound heterozygous model (CH), also 2-hits or multi-hits models, or recessive model.
	M5: CH model with weighted sum on the rare variants that form compound heterozygotes, i.e. a hybrid of M4 and M2		wCH: CH model with weighted sum on the rare variants that form compound heterozygotes, i.e. a hybrid of M4 and M2
	M6: 2-allele additive model where haplotypes are classified into two alleles, one with rare variants and one with all common alleles		2AD: 2-allele additive model where haplotypes are classified into two alleles, one with rare variants and one with all common alleles

	== Usage ==		== Usage ==

2014-09-18T04:54:09Z

Download

← Older revision		Revision as of 00:54, 18 September 2014
Line 126:		Line 126:

	== Download ==		== Download ==
	Source code of v0.01 [[Media:gtdt.0.01.tar.gz \| download]] here. A pre-compiled binary version v0.01 [[Media:gtdt.0.01.gz \| download]] here.		Source code of v0.01 [[Media:gtdt.0.01.tar.gz \| download]] here. A pre-compiled binary version v0.01 [[Media:gtdt.0.01.binary.gz \| download]] here.

	== Contact ==		== Contact ==
	For questions please contact the authors (Bingshan Li: [mailto:bingshan.li@vanderbilt.edu bingshan.li@vanderbilt.edu])		For questions please contact the authors (Bingshan Li: [mailto:bingshan.li@vanderbilt.edu bingshan.li@vanderbilt.edu])

2014-09-18T04:51:50Z

Download

← Older revision		Revision as of 00:51, 18 September 2014
Line 126:		Line 126:

	== Download ==		== Download ==
	Source code of v0.01 [[Media:gtdt.0.01.tar.gz \| download]] here. A pre-compiled binary version v0.01 ~~can be~~ [[Media:gtdt.0.01.gz \| download]] here.		Source code of v0.01 [[Media:gtdt.0.01.tar.gz \| download]] here. A pre-compiled binary version v0.01 [[Media:gtdt.0.01.gz \| download]] here.

	== Contact ==		== Contact ==
	For questions please contact the authors (Bingshan Li: [mailto:bingshan.li@vanderbilt.edu bingshan.li@vanderbilt.edu])		For questions please contact the authors (Bingshan Li: [mailto:bingshan.li@vanderbilt.edu bingshan.li@vanderbilt.edu])

2014-09-18T04:51:20Z

Download

← Older revision		Revision as of 00:51, 18 September 2014
Line 126:		Line 126:

	== Download ==		== Download ==
	Source code of v0.01 [[Media:gtdt.0.01.tar.gz \| download]] here.		Source code of v0.01 [[Media:gtdt.0.01.tar.gz \| download]] here. A pre-compiled binary version v0.01 can be [[Media:gtdt.0.01.gz \| download]] here.

	== Contact ==		== Contact ==
	For questions please contact the authors (Bingshan Li: [mailto:bingshan.li@vanderbilt.edu bingshan.li@vanderbilt.edu])		For questions please contact the authors (Bingshan Li: [mailto:bingshan.li@vanderbilt.edu bingshan.li@vanderbilt.edu])

2014-09-18T04:42:27Z

← Older revision		Revision as of 00:42, 18 September 2014
Line 124:		Line 124:
	'''p_2a_add''': p-value of M6		'''p_2a_add''': p-value of M6
	'''z_2a_add''': z-score of M6		'''z_2a_add''': z-score of M6

			== Download ==
			Source code of v0.01 [[Media:gtdt.0.01.tar.gz \| download]] here.

	== Contact ==		== Contact ==
	For questions please contact the authors (Bingshan Li: [mailto:bingshan.li@vanderbilt.edu bingshan.li@vanderbilt.edu])		For questions please contact the authors (Bingshan Li: [mailto:bingshan.li@vanderbilt.edu bingshan.li@vanderbilt.edu])

2014-09-04T17:25:25Z

Input

@@ Line 72: / Line 72: @@
   A disease_A
-* A VCF file [[http://www.1000genomes.org/node/101 VCF specs]]. It can contain variant information for more individuals than in the ped file.
+* A VCF file [[http://www.1000genomes.org/node/101 VCF specs]]. It can contain variant information for more individuals than in the ped file. The genotypes in the VCF file can be either phased or unphased. If unphased, gTDT will phased the genotypes by transmission.
-* The genotypes in the VCF file can be either phased or unphased. If unphased, gTDT will phased the genotypes by transmission.
+* A group file indicating which variants should be analyzed as a unit. It has required 3 columns, plus additional columns for weighting and others. For example:
 == Output ==

2014-09-04T17:20:06Z

Usage

← Older revision		Revision as of 13:20, 4 September 2014
Line 12:		Line 12:
	== Usage ==		== Usage ==

	A command gtdt without any input will invoke ~~triodenovo~~ and display the following message		A command gtdt without any input will invoke gtdt and display the following message

	The following parameters are available. Ones with "[]" are in effect:		The following parameters are available. Ones with "[]" are in effect:

2014-09-04T17:19:55Z

Usage

← Older revision		Revision as of 13:19, 4 September 2014
Line 12:		Line 12:
	== Usage ==		== Usage ==

	A command without any input will invoke triodenovo and display the following message		A command gtdt without any input will invoke triodenovo and display the following message

	The following parameters are available. Ones with "[]" are in effect:		The following parameters are available. Ones with "[]" are in effect:
Line 57:		Line 57:

	gtdt -p fam.ped -d fam.dat -g input.grp -v input.vcf -o out.txt --min_dp 10		gtdt -p fam.ped -d fam.dat -g input.grp -v input.vcf -o out.txt --min_dp 10



	== Input ==		== Input ==

2014-09-04T17:19:25Z

Introduction

← Older revision		Revision as of 13:19, 4 September 2014
Line 1:		Line 1:
	== Introduction ==		== Introduction ==
	* gTDT implemented gene-based or group-wise TDT for rare variant aggregation analysis. Currently gTDT implemented 6 tests for 6 models, M1-M6. It takes as input a ped file and a dat file that specify the relationships, and a VCF file that stores genotype data.		* gTDT implemented gene-based or group-wise TDT for rare variant aggregation analysis. Currently gTDT implemented haplotype-based tests for 6 models, M1-M6. It takes as input a ped file and a dat file that specify the relationships, and a VCF file that stores genotype data.

	* The 6 models are described as follows		* The 6 models are described as follows